Genome Assembly & Annotation
The genome assembly was produced by the Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University. The assembly uses Illumina HiSeq4000 paired-end sequencing. The reads were assembled with shovil pipeline 1.0-pre1. Decontamination was performed using BLAST against UniRef90. Scaffolding was performed with BESST. Gaps were filled with the GAPCLOSER software. The mitochondrial genome was assembled with mitobim.
Gene models were provided by the Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University. Different ab initio/evidence-based gene prediction were combined to obtain gene models: Geneid, glimmerHMM, GeneMarkES, geneMarkET and SNAP, using a combination of external RNASeq data, training gene models produced by PASA pipeline and PASA-derived transcript evidence. A very thorough procedure had been followed to combine the output of the above methods and produce the final gene models. More details can be found here.
- Konczal M, Przesmycka KJ, Mohammed RS, Phillips KP, Camara F, Chmielewski S, Hahn C, Guigo R, Cable J, Radwan J. Gene duplications, divergence and recombination shape adaptive evolution of the fish ectoparasite Gyrodactylus bullatarudis. Mol Ecol, 2020;29(8):1494-1507
|Adam Mickiewicz University
This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh